A Change in NCIS
by MetallicMilitia
Summary: What If Kate Todd wasn't the one to be shot on the roof, what if Tony got hit non-fatally, what if they loved each other! Rated M to be safe
1. Chapter 1

A Change in NCIS

Chapter 1: What if

By: MM

Disclaimer: I do not own anything but the story plot here, nor do I want to, too troublesome.

A/N: So my favorite TV show of all time has been NCIS and I have to say that I love some weird pairings in the show like Tony and Abby or Tony and Kate, but anyway this story has been in my head since like forever, and it needs to come out. This is a Tony Kate story; there will be another Tony Abby one on later. This starts on the scene when Kate gets shot but there will be a twist.

Rated M for mild violence, some graphic language, and just ordinary precautions

Gibbs looked around on the top of the building Tony was walking over to Kate to help her up. Kate was smiling and accepting Tony's hand, when the phone rang. Gibbs flipped the phone open and answered with his usual, "Gibbs", but the chilling voice on the phone was enough to send a shiver down his spine.

"Well seeing as I couldn't do my job in killing you special agent Gibbs, I'll have to leave knowing that I still hurt you in a way that you will never forget." Ari spoke coldly over the phone.

Gibbs somehow deciphered what he was talking about, "Tony get Kate down NOW!" Now everyone here expects a slowdown, well don't believe it. The following all happened within moments of each other. Tony heard what Gibbs said and looped his right boot behind Kate's left and pushed. She started falling backwards, but since Tony was in a weird stance he would have to dive to the left, and he did, but halfway through the dive, the murderous bang was sounded. Tony thudded to the floor and did not move another inch.

Kate who had been slowed down because of the previous shot to her chest did not register what was going on until she was already on the ground, that's when she heard the thunderous clap of a gun. She had a front row seat to what happened, halfway through his dive Tony jerked unnaturally then hit the floor not moving or even making a sound, the usually cheery and talkative Tony, was silent. Kate started crawling over to him. She heard him gasp and then he coughed. She flipped him to his back considering he landed face down, and that's when she noticed the blood coming out of his side, and coming out of his mouth, he looked unconscious, but still trying to cling on to life.

What nobody knew until later was that Tony had hesitated before diving to shield Kate until he knew she was down, this made Ali confused, he was going to shoot him in the head when he dove _right_ after he pushed. So as he moved the scope back to Tony, that is when he jumped, so Ali had to move with the jump and fire, he knew the head shot was gone, but maybe he could still hit the heart or some other vital organ. However because of Tony's hesitance it saved not only his own life but Kate's as well, not that anyone knew that of course.

"Tony … Tony come on … Tony please you survived the plaque, don't die from this … O God … TONY!" Kate was hysterical now. She was crying as she was applying pressure to the wound, but the blood was still coming.

Gibbs after hearing the scream feared the worst and ran over to the spot ignoring all the danger. He saw Tony bleeding from his side and what appeared to be his stomach area, Kate was doing her best to try and keep air out of his diaphragm, so he could breathe. Gibbs radioed down to McGee, "Call for an ambulance and tell them to get here ASAP … Agent Down … he needs immediate medical attention."

McGee was stunned to silence for a second 'Agent down but … he said he … No it can't be Tony … Aw shit Tony.' With the thought of Tony hurt McGee got to work immediately.

At this point Tony started coming to, his eyes looked around, and that's when he noticed Kate hovering over him. She was crying, and god, he did not like that sight. He needed to stop her from crying, so he tried comforting her, as best he could with his left hand he reached up and stroked away some of her black hair and rubbed her right check. Kate looked him in the face and he smiled softly at her. He moved his right hand over Kate's. He then used his left thumb and cleared away some of the tears. He promptly passed out after that, as he used up the remainder of his energy to do this.

Kate continued to stare at Tony's face. She didn't know what she would do if he died on her. Agent Kate was a veteran to death when she worked as Secret Service, but she was a greenhorn to this, the bond she shared with Tony was incredible, and here she was again, watching him silently as he slowly dies. First the plaque, then the car bomb that he saved them from, and now … now he was bleeding out onto her and the roof of the building that they were on.

Gibbs looked at the police helicopter as it flew overhead to the location that was thought to have been Ali's. Gibbs knew that Tony needed help and pronto. "McGee, can we contact that helicopter." After a brief pause McGee responded, "Boss I'm patching you through now, go for it."

"This is Special Agent Leroy Jethro Gibbs, to police helicopter serial number 5, Charlie, Delta, 2, 2, Fox trot, can you read me over."

"Loud and clear Leroy, we are looking for your shooter now, so far no traces however."

"Never mind that he's gone, can you take a passenger? We have a downed agent in need of medical attention."

"Affirmative, we will take your agent, we cannot land however, it will be a touch and go, James in the back happens to be an EMT, your man will be in good hands."

The helicopter rounded once, and during this time Gibbs pulled Tony into a cradle with Kate still applying pressure to the wound. The Helicopter then came low Kate moved away, and Gibbs took off in a full sprint for the helicopter. The back door slid open and just in time, Gibbs just reached the door and placed Tony down, the man, James, looked shocked at first, but then got right to work. Gibbs then shut the door patted the side and ran off back to Kate as the helicopter took off and headed to the closest hospital.

Gibbs looked at Kate and noticed that she was pale and covered in Tony's blood, he took his jacket off and handed draped it over her shoulders. Their job where done, now was the time to worry for Tony's safety. Gibbs walked Kate all the way down the stairs. He exited first and there was McGee, worry plastered all over his face, it then went pale. Kate had just stepped out of the building. Blood was caked on her shirt and her right check, her arms and hands just crimson due to the pressure she tried to give for Tony. No one said a word. They got in the car and headed for NCIS HQ, to get cleaned up, debriefed, and to inform everyone.

It was a completely silent ride. Not a word. Kate was looking at the headrest of the seat in front of her. McGee sat in the passenger seat looking out the side window, and Gibbs driving. Silent, that's how it seemed, but their minds where racing, worry for Tony, how to tell everyone, what was going to happen next, in fact what hospital was he taken to. The was something else thought, for Gibbs it was about failure to protect, McGee, sorrow for not being there, and for Kate who was taking all of this the hardest, anger toward Ali, and herself for not understanding the situation.

The car pulled to a stop and the three got out and walked into the awaiting elevator. Then the ding was sounded. Kate and McGee got off and headed to the locker room. Gibbs was still going up. Another Ding, the doors opened. Gibbs stepped out to see the looks of everyone in NCIS, Abby ran over and hugged Gibbs, but unlike Gibbs, he didn't hug back. Abby started worrying. "Gibbs what's wrong, where's Tony, Kate, and McGee? O No which one, o god no, No, No, no."

"Abs … Tony was hit … he's being treated as we speak … Kate and McGee are downstairs." Gibbs was interrupted by another ding. And again the elevator doors opened, everyone gasped. Kate stood there covered in blood, walked over to Gibbs, "Where is he?" The question barely a whisper. It was a defeated tone, no happiness, no fun, nothing, it was sad and pain filled. Abby dropped to her knees and started crying, harder then she had ever. Ducky walked over and took a hold of Abby and stood her up and walked her with Gibbs and Kate toward the director's office. It was there that they would learn which hospital was caring for Tony.

The team was dismissed everyone headed for the hospital, however back at NCIS the director had to make an announcement. "Everyone today we have suffered something that could have been worse. Thanks to the quick thinking of a Special Agent, he saved another at the cost of being shot. He has been on leave for a few days now due to him being exposed to the Plaque. He also saved his squad from a deadly car bomb. For the remainder of the day as you may leave now, I want you all to be thinking of him, and please wish him well. … That is all."

There they were the NCIS team, sitting in a waiting room by themselves, Abby crying, Ducky trying to help her. Everyone else was sitting around it was about an hour later that a doctor entered the room. "Well some good news, Tony will make a full recovery, the bad news is that he will not recover nearly as fast due to the other problems that he has now. You all would like to see him correct, well I'm sorry to say that he is sleeping at the moment and that we would like that he continues, however when he awakens I will let you know and have you visit him. Any questions?" It was surprising but it was Abby that asked the first question. "How bad was the wound, doctor?" The doctor bowed his head for a second. "To tell the truth it was complicated, when the bullet entered his body it traveled in and hit one of his ribs, this of course would mean that it would normally go through the rib, but instead it broke the rib and pushed it into his left lung, the bullet then broke into two pieces the larger piece exited the lower chest cavity while the other exited right by the entrance wound. He is lucky to be alive. Normally the bullet would have gone through the rib into the lung and then proceed to the other while hitting major arteries and similar organs. Tony is a lucky man, but he will have a scar that will remain the rest of his natural life. He lost a lot of blood and Kate you probably saved his life by applying pressure to his wound and Gibbs same to you for calling in the helicopter."

The whole room felt a small wave of relief from the doctor's words, but Kate was still anxious to see him. They continued sitting there waiting for the word that they could see him. Some small talk was going on in the room now but it was Gibbs and Kate that remained silent. Ducky knew better than to point that out and continued talking with Abby to try and lighten her mood.

A few hours went by and finally a nurse entered the room, "He has woken up please though do not rush him, in fact you should go one at a time would that be alright." Abby went first than McGee, Ducky, and then Gibbs. Kate decided to go last since she wanted to stay with him period. Kate followed the nurse all the way to the room that he was in.

She walked into the room and he looked over and smiled. "Tony." She whispered

"Hey Kate" Tony said sweetly.

"You always have to get hurt don't you?" Kate asked playfully.

Tony smiled "Ya I'm that type of person I guess."

Kate smiled, "You know Tony, there is something I need to say that goes along with that, Tony you are who you are and that is amazing, Tony your always looking out for your friends and everything … Tony I … I Love that about you, I love you."

Tony smiled brightly, "huh, McProbbie was saying something like that earlier. Kate I love you too so very much, but remember rule number 12, no dating your teamma-" Tony was cut off by Kate as she had walked over and smashed her lips into his.

"Some rules are meant to be broken agent DiNozzo." Kate said with a smile after she broke the kiss.

Tony laid there with a smile on his face, "Kate, with you everything seems so much different, Katie if I had a ring right now, I'd drop to my knee and propose."


	2. A Question for the Readers

A Change in NCIS

By: MM

A Quick question for you readers, Would you like for me to continue this or should I keep this story a one – shot based story, I liked how it went to tell the truth but, I'm not sure if I will be able to keep it up and keep the story at such a good pace and keep to the main plot, even though I have watched every single episode of the show. Respond In any form you would like.


	3. It Will Continue

MM here thank you everyone I will continue the story soon again thank you.


	4. Chapter 2

A Change in NCIS

Chapter 2: Revealed Truth

By: MM

Disclaimer: I do not own anything but this story plot, nor would I want to, too troublesome.

A/N: Even though this story has hardly any views I still won't get discouraged thanks for the support. Also please help with suggestions or ideas or this story will die.

Rated M for graphic language, violence, and just to be safe.

Tony was lying in bed as Kate described in lame man terms how he survived. Gibbs had come in periodically to check up on his senior agent. Tony had complained about how he hated hospitals ever since he broke his arm back when he was twelve. As the day progressed Gibbs came in at one point and smirked at the two agents and laughed when they had sputtered when he asked when the wedding day would be and if he would be included in the ceremony. He winked at them and told them that he supported their relationship and that he would make an exception to rule 12. However he told them that he would strictly be no emotions or drama at work, which had to be left at home.

Kate kissed Tony's check that night and he smile brightly and grabbed her hand as she tried walking out to leave for home. When she turned around to see what Tony he was pouting like a little child want the lollipop that are near the check out. "I want an actual kiss Katie not a check kiss or a peck a full on kiss." She smiled, and leaned down and kissed him, however unlike what Tony had though was going to happen she continued him, she then started running her hand up and down his chest, but carefully. She kept going lower and lower until she hit his waist line on his pants and removed her hand and her mouth. Tony's eyes were half lidded and he looked to wanting.

"Get better soon Tony." She stopped as she was walking toward the door as she sensually moved her hips, turned to face him winked and said "I'll be waiting."

It had been about a week and Tony was restless he had talked to the doctor and he had said that, Tony would be leaving today, funny think was his dad had actually caught wind of what had happened and had come and made things right between the two, during the week, his dad was there and would be taking Tony home. As the two were getting into the car as tony had been wheeled out to the car, as Tony's dad was pulling out Tony had asked to go to NCIS. His dad had agreed and they headed to the building. As Tony entered the bullpen he couldn't see any of his team there, that is when the director came down the stairs, "Tony how are you feeling?"

"I'm doing fine, just here to say hi to everyone then heading home to watch some old movies with my father." Tony answered while looking at the bullpen.

Shepard smiled, "They got called out to help with a stake out, nothing too big, actually Abby is here, she would be delighted to see you."

Tony smiled and nodded as he headed to the other elevator to head to Abby's lab. As the elevator dinged and he started toward the lab he could here Abby's music and when the door opened for him. Without looking Abby started talking.

"Hey, Gibbs what can I do for you." Tony smiled at that, and was about to chuckle when he came up with a joke and mocked Gibbs' voice.

"Have the tests come out, do the bullets match?" Abby turned around confused and when she saw Tony she grinned and ran over to him and hugged his arm.

"Tony!" she cried as she ran. "Are you feeling better, no lingering pain?"

"I'm fine Abbs, the pain killers are working fine. How are you I mean you were pretty shaken up with me getting hit?" Tony asked out of concern.

"Well because … well you'll let this go to head but I'll say it anyway, you're like my older brother so if anything happened to you or Kate, I don't know what I would do." Abby said, "So when I heard that you were shot I thought the worst, Tony first plaque, and then getting shot."

Tony laughed a little and said, "You forgot the car explosion, and nothing will keep me from my girls." Abby understood however, Tony had told her that he had a crush on Kate a few weeks ago that and she was always going to be his favorite Goth chick in the world.

Then they sat and talked for a little while until Tony got tired and kissed Abby's forehead and wished her a good night and headed home, once home Tony and his dad started watching a movie _First Blood_ and as normal Tony tried his best Stallone impersonation. After the movie Tony and his dad had some take out and Tony told his father to stay with him that the guest bedroom was never used.

As Tony walked into his room as his father left to go get his things at the Hotel that they were staying at. Tony had noticed something off as he walked into his room, the sheets were ruffled, he always made his bed, as he looked around for some more clues he noticed a shirt, he walked over to it picked it up and looked at it, he remembered it. Kate was wearing it the day before last. He chuckled Kate must have come by at some point and slept it was closer than her house and he had let her do it before. Tony walked over to his drawers and opened up the first one and pulled out his plaid pajama pants.

Tony then started to struggle to get his pants off and then back on. He was so in raptured with changing that he didn't notice that his front door had opened and that there where footsteps coming towards his room. He noticed however when a shadow covered the floor under his feet. He whirled around on the balls of his feet and prayed that it wasn't an intruder he didn't have his weapon, however the sight of Kate made all of his thoughts melt away.

Kate giggled when she had first saw that Tony had his tongue out in concentration while trying to button his pajama pants. Then when he whirled around to face her she knew that he hadn't even noticed that she was here, but then a delighted face flashed over his facial expressions. "Hey Tony, how are you feeling?"

"Well I'm fine but umm … can you help me with my shirt?" Tony asked sheepishly, Kate giggled because of this. Kate walked over to Tony and knew that this would be hard as to not aggravate his wound.

"Sit on the bed babe and I'll help you out." Tony did as asked and walked to his bed and sat down, Kate smiled as she followed him and started to unbutton his shirt and pull it back so it would roll of his shoulders and down his strong arms. A slight redness came to Kate's cheeks. She continued to look him up and down, his muscles even though they were covered by his bandages were defined. Kate reached over and put her hand on his chest.

Tony looked up to see what she was planning, and he smiled as she was smiling and her eyes shown happiness and contentment. "You're cute Kate DiNozzo."

Kate looked up surprised and Tony just smiled, "Only when there is a stone on my finger."

He smiled genuinely and said tiredly "Soon maybe." Kate looked at him too see that he really looked like that he needed some sleep.

"Tony, go to sleep alright." Kate said, Tony looked at her and nodded. Kate sighed, Tony wasn't himself quite yet, he lost a lot of strength and he gave up fights that he would have normally continued. "Alright well you're all set so I'm going to head out."

"No! I mean, no please stay with me, sleep with me," Tony said nearly forgetting that he was one tired and two Kate was her own person and she didn't actually have to stay.

Kate gently smiled and only nodded, "Just give me a minute to go get some of my things alright Tony."

"That's fine." Tony smiled. When Kate left the room however he felt like the room had gotten very boring and he was looking around for something to hold his attention to keep him awake until Kate came back. However he lost the fight very fast and he fell into a deep sleep almost immediately.

Kate walked into the bedroom to find Tony a sleep and looking peaceful as could be. She smiled and climbed into bed right next to the man that she loved and fell asleep also.

The next morning wasn't something Tony had expected how to wake up for a while. A cell phone buzzing, he was reaching for his before he knew any better and when he flipped open his phone and said his last name tiredly and got no response except for more ringing, he was confused.

That is he was confused until he heard a soft voice of someone he knew very well, he looked to the other side of him and saw the person that he loved like no other. She was on the phone and she nodded and said a few words that he did not want to hear from her at the moment.

"I'll be right there." Kate said. Gibbs had called because the guy they were staking out was apparently getting arrested for drug selling. So now that there was a warrant they had permission to search his house for the items that they needed to bust him for making a bomb threat to the Navy several days ago, he had said that he was planning to bomb one of their naval ships and he had demonstrated by sending them a video of his bomb being detonated.

Kate got up and kissed Tony on the check and he nodded, "I'll be fine, but when you're done and when you're on your way home grab a movie and come here." Kate smiled and nodded her head and went into his bathroom and changed and left. Tony on the other hand went back to sleep considering he honestly was not a morning person.

It had been a few hours and Tony was bored and the doctor had told him that he did need to exercise by walking, not just for the current wound, but from plague, so he decided that he would walk to NCIS and pick up Gibbs a coffee, Kate an espresso, McGee would get a cappuccino, and he would also pick up a Caf-Pow for Abbs.

When he got to NCIS he first went to Abby, she gave him a peck on the check and told him to go see the others. He agreed and went up the elevator. When he got up to the bullpen nobody was there until he saw Gibbs walking down the stairs from the director's office and he did not look too happy.

"Hey Boss got you your coffee just the way you like it." Gibbs saw it and smiled at Tony. He walked forward and accepted the drink with a smile and rubbed Tony's head. "Where are the others?"

"Interrogation, the bastard won't admit to anything yet. We aren't in charge of anything at the moment so we can't even ask him we have to wait for the police to finish." Gibbs sighed as he started toward the rooms.

Tony followed right behind and chuckled him and Gibbs both agreed on that, Politics were foolish. When Tony entered the room he tapped McGee and handed him his drink. "Where's Kate?"

"She just stepped out to use the restroom. It's been a long day thanks for the coffee." McGee said as he took a sip. So Tony waited and when Kate entered the room she looked at Tony with a surprised face and smiled when she was handed her favorite drink on a long case.

"Shouldn't you be home, not that I don't appreciate the gift Tony?" Kate said curious.

"Well I walked here, I have to in order to get my lungs back to normal, you know with Black Death it can do that to you." Tony remarked

"What about your new wound won't it stress it?" McGee asked worried.

"No, not after this long." Gibbs answered before Tony could open his mouth; Gibbs then looked at Tony for a moment and looked back toward the guy in the other room being interrogated however, Tony caught the slight frown on his face. It was starting to bug him; he saw it earlier when Gibbs walked past him toward Interrogation.

"Hey, Boss can we talk?" Tony asked his curiosity getting the better of him.

Gibbs contemplated a smart remark like 'we already are' but decided to be serious. "Ya come on." So Gibbs lead Tony out of the room and back through the bullpen and to the elevator. Once the doors opened and they were inside and the doors shut he hit the switch, "My guess is that you wanted privacy."

"Um, well, I was actually wondering what was going on, you came down from the director's office pretty upset, that and whenever you looked at me you smile more than usual and frown right after when you thought that nobody would see?"

Gibbs grunted, "You're too observant Tony." After a few moments Gibbs looked at his Senior Field Agent, "Unfortunately Tony I have bad news. Jenny has you going on a deep cover operation as soon as you get back, now normally I would not give this a second thought; however, it's what and why you will be doing it especially after getting together with Kate."

"It is more of a revenge topic and you are to get the daughter of a certain man to fall in love with you, now understand, you will be moved to a different country."

Tony was shocked, well that was more of an understatement, but what could he do.

"Now Tony go be with Kate alright, enjoy your time with her. Since once this operation starts, you won't have much time together.

Alright sorry for the wait and also sorry for the short chapter, it was to build up for the next chapter, also I would love for ideas and suggestions, please, this story will not make it without you the reader's input. So please, please, please, help me to entertain you. MM says until next time peace.


End file.
